Thanks! Based on your feedback this works. It never ceases to amaze me what perl can do! I'm first preserving the ASCII portion of the file other purposes.

#!/usr/local/bin/perl
use strict;
use warnings;

my $raw_file="spectrebin.raw";

open (FILE,$raw_file);

foreach my $line (<FILE>) {
   if ($line=~/^Binary:/) {
      #Do not read the binary part as ascii
      printf "ASCII: $line";
      last;
   } else {
      #the ascii part
      printf "ASCII: $line";
   }
}
close(FILE);

open (FILE,$raw_file);  
binmode(FILE) or die "ERROR> Could not read binary file";

$/ = "Binary:\n";
my $text = <FILE>;

my $buffer;
while ((read (FILE, $buffer, 64))!=0) {
   my $binary = unpack("B64",$buffer);
   printf "Binary: $binary\n";
}
close(FILE);
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